./ install/ install/doinst.sh install/slack-desc usr/ usr/bin/ usr/doc/ usr/doc/snpEff-4.3t/ usr/doc/snpEff-4.3t/References usr/doc/snpEff-4.3t/snpEff.SlackBuild usr/share/ usr/share/java/ usr/share/java/snpEff/ usr/share/java/snpEff/SnpSift.jar usr/share/java/snpEff/examples/ usr/share/java/snpEff/examples/1kg.head_chr1.filtered.vcf.gz usr/share/java/snpEff/examples/1kg.head_chr1.vcf.gz usr/share/java/snpEff/examples/cancer.ann.vcf usr/share/java/snpEff/examples/cancer.eff.vcf usr/share/java/snpEff/examples/cancer.vcf usr/share/java/snpEff/examples/cancer_pedigree.ann.vcf usr/share/java/snpEff/examples/cancer_pedigree.vcf usr/share/java/snpEff/examples/example_motif.vcf usr/share/java/snpEff/examples/examples.sh usr/share/java/snpEff/examples/file.vcf usr/share/java/snpEff/examples/intervals.bed usr/share/java/snpEff/examples/my_annotations.bed usr/share/java/snpEff/examples/samples_cancer.txt usr/share/java/snpEff/examples/samples_cancer_one.txt usr/share/java/snpEff/examples/test.1KG.ann_encode.vcf usr/share/java/snpEff/examples/test.1KG.ann_reg.vcf usr/share/java/snpEff/examples/test.1KG.vcf usr/share/java/snpEff/examples/test.ann.vcf usr/share/java/snpEff/examples/test.chr22.ann.filter_missense.vcf usr/share/java/snpEff/examples/test.chr22.ann.filter_missense_any.vcf usr/share/java/snpEff/examples/test.chr22.ann.filter_missense_any_TRMT2A.vcf usr/share/java/snpEff/examples/test.chr22.ann.filter_missense_first.vcf usr/share/java/snpEff/examples/test.chr22.ann.one_per_line.txt usr/share/java/snpEff/examples/test.chr22.ann.txt usr/share/java/snpEff/examples/test.chr22.ann.vcf usr/share/java/snpEff/examples/test.chr22.vcf usr/share/java/snpEff/examples/test.vcf usr/share/java/snpEff/examples/variants_1.ann.vcf usr/share/java/snpEff/examples/variants_1.vcf usr/share/java/snpEff/examples/variants_2.ann.vcf usr/share/java/snpEff/examples/variants_2.vcf usr/share/java/snpEff/galaxy/ usr/share/java/snpEff/galaxy/snpEff.xml usr/share/java/snpEff/galaxy/snpEffWrapper.pl usr/share/java/snpEff/galaxy/snpEff_download.xml usr/share/java/snpEff/galaxy/snpSiftWrapper.pl usr/share/java/snpEff/galaxy/snpSift_annotate.xml usr/share/java/snpEff/galaxy/snpSift_caseControl.xml usr/share/java/snpEff/galaxy/snpSift_filter.xml usr/share/java/snpEff/galaxy/snpSift_int.xml usr/share/java/snpEff/galaxy/tool-data/ usr/share/java/snpEff/galaxy/tool-data/snpEff_genomes.loc usr/share/java/snpEff/galaxy/tool-data/snpEff_genomes.loc.sample usr/share/java/snpEff/galaxy/tool_conf.xml usr/share/java/snpEff/galaxy/tool_dependencies.xml usr/share/java/snpEff/scripts/ usr/share/java/snpEff/scripts/1kg.sh usr/share/java/snpEff/scripts/annotate_demo.sh usr/share/java/snpEff/scripts/annotate_demo_GATK.sh usr/share/java/snpEff/scripts/bedEffOnePerLine.pl usr/share/java/snpEff/scripts/buildDbNcbi.sh usr/share/java/snpEff/scripts/cgShore.pl usr/share/java/snpEff/scripts/cgShore.sh usr/share/java/snpEff/scripts/countColumns.py usr/share/java/snpEff/scripts/db.pl usr/share/java/snpEff/scripts/extractSequences.pl usr/share/java/snpEff/scripts/fasta2tab.pl usr/share/java/snpEff/scripts/fastaSample.pl usr/share/java/snpEff/scripts/fastaSplit.pl usr/share/java/snpEff/scripts/fastqSplit.pl usr/share/java/snpEff/scripts/filterBy.py usr/share/java/snpEff/scripts/gffRemovePhase.pl usr/share/java/snpEff/scripts/gsa/ usr/share/java/snpEff/scripts/gsa/bayesFactor_correction_scoreCount.r usr/share/java/snpEff/scripts/gsa/bayesFactor_correction_scoreCount.sh usr/share/java/snpEff/scripts/gsa/bayesFactor_correction_scoreCount_max10.sh usr/share/java/snpEff/scripts/gsa/checkGeneNames.py usr/share/java/snpEff/scripts/gsa/create_sets.bds usr/share/java/snpEff/scripts/gsa/geneSetOverlap.py usr/share/java/snpEff/scripts/gsa/geneSetOverlap.sort.txt usr/share/java/snpEff/scripts/gsa/geneSetsGtex.py usr/share/java/snpEff/scripts/gsa/pvalue_correction_scoreCount.r usr/share/java/snpEff/scripts/gsa/pvalue_correction_scoreCount.sh usr/share/java/snpEff/scripts/gsa/pvalue_correction_scoreCount_min10.sh usr/share/java/snpEff/scripts/isutf8.py usr/share/java/snpEff/scripts/join.pl usr/share/java/snpEff/scripts/joinSnpEff.pl usr/share/java/snpEff/scripts/make_dbNSFP.sh usr/share/java/snpEff/scripts/nextProt_filter.pl usr/share/java/snpEff/scripts/ped2vcf.py usr/share/java/snpEff/scripts/plot.pl usr/share/java/snpEff/scripts/plotHistogram.pl usr/share/java/snpEff/scripts/plotLabel.pl usr/share/java/snpEff/scripts/plotMA.pl usr/share/java/snpEff/scripts/plotQQ.pl usr/share/java/snpEff/scripts/plotQQsubsample.pl usr/share/java/snpEff/scripts/plotSmoothScatter.pl usr/share/java/snpEff/scripts/plotXY.pl usr/share/java/snpEff/scripts/queue.pl usr/share/java/snpEff/scripts/sam2fastq.pl usr/share/java/snpEff/scripts/snpEff usr/share/java/snpEff/scripts/snpSift_filter_sample_to_number.pl usr/share/java/snpEff/scripts/sortLine.py usr/share/java/snpEff/scripts/splitChr.pl usr/share/java/snpEff/scripts/statsNum.pl usr/share/java/snpEff/scripts/swapCols.pl usr/share/java/snpEff/scripts/transpose.pl usr/share/java/snpEff/scripts/txt2fa.pl usr/share/java/snpEff/scripts/txt2vcf.py usr/share/java/snpEff/scripts/uniqCount.pl usr/share/java/snpEff/scripts/uniqCut.pl usr/share/java/snpEff/scripts/vcfAnnFirst.py usr/share/java/snpEff/scripts/vcfBareBones.pl usr/share/java/snpEff/scripts/vcfEffHighest.ORI.py usr/share/java/snpEff/scripts/vcfEffOnePerLine.pl usr/share/java/snpEff/scripts/vcfFilterSamples.pl usr/share/java/snpEff/scripts/vcfInfoOnePerLine.pl usr/share/java/snpEff/scripts/vcfOnlyAlts.pl usr/share/java/snpEff/scripts/vcfReduceGenotypes.pl usr/share/java/snpEff/scripts/vcfRefCorrect.py usr/share/java/snpEff/scripts/wigSplit.pl usr/share/java/snpEff/snpEff.config usr/share/java/snpEff/snpEff.jar s_1.vcf inflating: snpEff/examples/example_motif.vcf inflating: snpEff/examples/cancer_pedigree.ann.vcf inflating: snpEff/examples/test.1KG.ann_encode.vcf inflating: snpEff/examples/file.vcf inflating: snpEff/examples/variants_2.ann.vcf inflating: snpEff/examples/test.1KG.ann_reg.vcf creating: clinEff/ inflating: clinEff/clinEff.config inflating: clinEff/ClinEff.jar inflating: clinEff/workflow.config creating: clinEff/workflow/ inflating: clinEff/workflow/workflow.config inflating: clinEff/workflow/workflow.GRCh38.config creating: clinEff/report/ creating: clinEff/report/bootstrap/ inflating: clinEff/report/bootstrap/bootstrap.min.js inflating: clinEff/report/bootstrap/bootstrap.min.css inflating: clinEff/report/reportlof.html.flt inflating: clinEff/report/reportclinical.html.flt inflating: clinEff/report/style.css creating: clinEff/report/img/ inflating: clinEff/report/img/logo.png inflating: clinEff/report/img/logo_example_ori.png extracting: clinEff/report/img/logo_example.png inflating: clinEff/report/reporthighimpact.html.flt /usr/src/slapt-src/academic/snpEff/snpEff Slackware package maker, version 3.14159265. Searching for symbolic links: usr/bin/SnpSift.jar ../share/java/snpEff/SnpSift.jar usr/bin/snpEff.jar ../share/java/snpEff/snpEff.jar Making symbolic link creation script: ( cd usr/bin ; rm -rf SnpSift.jar ) ( cd usr/bin ; ln -sf ../share/java/snpEff/SnpSift.jar SnpSift.jar ) ( cd usr/bin ; rm -rf snpEff.jar ) ( cd usr/bin ; ln -sf ../share/java/snpEff/snpEff.jar snpEff.jar ) It is recommended that you make these lines your new installation script. Would you like to make this stuff the install script for this package and remove the symbolic links ([y]es, [n]o)? y Removing symbolic links: removed './usr/bin/snpEff.jar' removed './usr/bin/SnpSift.jar' Creating your new ./install/doinst.sh... This next step is optional - you can set the directories in your package to some sane permissions. If any of the directories in your package have special permissions, then DO NOT reset them here! Would you like to reset all directory permissions to 755 (drwxr-xr-x) and directory ownerships to root.root ([y]es, [n]o)? n Creating Slackware package: /usr/src/slapt-src/academic/snpEff/snpEff-4.3t-noarch-1salix15.0.txz Slackware package /usr/src/slapt-src/academic/snpEff/snpEff-4.3t-noarch-1salix15.0.txz created. Installing package snpEff-4.3t-noarch-1salix15.0... | snpEff (Genetic variant annotation and effect prediction toolbox) | | SnpEff is a variant annotation and effect prediction tool. It | annotates and predicts the effects of variants on genes (such | as amino acid changes). | | Home: http://snpeff.sourceforge.net/ | | | | | |